Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
GBM8
NA
NA

Attributes by original data submitter

Sample

source_name
low-passage glioma-initiating stem-like cells (GBM8)
cell type
low-passage glioma-initiating stem-like cells (GBM8)
chip antibody
CTCF (#3418, Cell Signaling)
treatment
treated with Pool of 4 siRNA against HOXD-AS2 for 48 hours

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7546S, NEB). ChIP-Seq with Drosophila spike-in chromatin (Cat. 53083, Active Motif) and Drosophila -specific histone variant, H2Av (Cat. 61686, Active Motif) were added to each sample prior IP for normalization.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
9810818
Reads aligned (%)
83.3
Duplicates removed (%)
13.0
Number of peaks
4814 (qval < 1E-05)

hg19

Number of total reads
9810818
Reads aligned (%)
82.2
Duplicates removed (%)
15.7
Number of peaks
4872 (qval < 1E-05)

Base call quality data from DBCLS SRA